Difference between revisions of "Track coverage (analysis)"

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(Default analysis icon as separate file)
 
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;Analysis title
 
;Analysis title
:[[File:Track-coverage-analysis-icon.png]] Track coverage
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:[[File:Default-analysis-icon.png]] Track coverage
 
;Provider
 
;Provider
 
:[[Institute of Systems Biology]]
 
:[[Institute of Systems Biology]]
 +
;Class
 +
:{{Class|ru.biosoft.bsa.analysis.TrackCoverageAnalysis}}
 
;Plugin
 
;Plugin
 
:[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]
 
:[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]
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* '''Sequences''' – Collection of sequences
 
* '''Sequences''' – Collection of sequences
 
** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually
 
** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually
** '''Sequence collection''' – Sequence collection
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** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected
** '''Genome ID string''' – Something like <nowiki>'</nowiki>hg18<nowiki>'</nowiki> or <nowiki>'</nowiki>mm6<nowiki>'</nowiki>
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* '''Window size''' – Size of the window to average the coverage
 
* '''Window size''' – Size of the window to average the coverage
 
* '''Step''' – Number of bp to step (at least 1000)
 
* '''Step''' – Number of bp to step (at least 1000)

Latest revision as of 18:07, 14 June 2013

Analysis title
Default-analysis-icon.png Track coverage
Provider
Institute of Systems Biology
Class
TrackCoverageAnalysis
Plugin
ru.biosoft.bsa (Bio-sequences analyses plugin)

[edit] Description

Calculates the coverage of given track

[edit] Parameters:

  • Input track – Track to calculate coverage for
  • Sequences – Collection of sequences
    • Sequences source – Select database to get sequences from or 'Custom' to specify sequences location manually
    • Sequence collection – Specify path to folder containing sequences if 'Custom' sequences source is selected
  • Window size – Size of the window to average the coverage
  • Step – Number of bp to step (at least 1000)
  • Output empty intervals – When checked, intervals without single site will appear in the output table as well
  • Output table – Path to the output table
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